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You Xu
You Xu
Westlake University
Verified email at westlake.edu.cn
Title
Cited by
Cited by
Year
Estimation of ADME properties with substructure pattern recognition
J Shen, F Cheng, Y Xu, W Li, Y Tang
Journal of chemical information and modeling 50 (6), 1034-1041, 2010
3382010
Additive CHARMM force field for naturally occurring modified ribonucleotides
Y Xu, K Vanommeslaeghe, A Aleksandrov, AD MacKerell Jr, L Nilsson
Journal of computational chemistry 37 (10), 896-912, 2016
732016
Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations
Z Shen, F Cheng, Y Xu, J Fu, W Xiao, J Shen, G Liu, W Li, Y Tang
PloS one 7 (3), e33500, 2012
482012
LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures
YV Pabon-Martinez, Y Xu, A Villa, KE Lundin, S Geny, CH Nguyen, ...
Scientific Reports 7 (1), 11043, 2017
372017
Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima
E Morgunova, Y Yin, PK Das, A Jolma, F Zhu, A Popov, Y Xu, L Nilsson, ...
Elife 7, e32963, 2018
352018
Computational insights into the different catalytic activities of CYP2A13 and CYP2A6 on NNK
Y Xu, Z Shen, J Shen, G Liu, W Li, Y Tang
Journal of Molecular Graphics and Modelling 30, 1-9, 2011
192011
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields
Y Ding, Y Xu, C Qian, J Chen, J Zhu, H Huang, Y Shi, J Huang
Journal of computer-aided molecular design 34 (4), 421-435, 2020
102020
The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid
Y Xu, A Villa, L Nilsson
Journal of Computational Chemistry 38 (15), 1147-1157, 2017
102017
Structural effects of modified ribonucleotides and magnesium in transfer RNAs
Y Xu, AD MacKerell Jr, L Nilsson
Bioorganic & medicinal chemistry 24 (20), 4826-4834, 2016
102016
The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study
Y Xu, O Gissberg, YV Pabon-Martinez, J Wengel, KE Lundin, CIE Smith, ...
PLoS One 14 (2), e0211651, 2019
92019
Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures
Y Xu, J Huang
Communications Chemistry 4 (1), 99, 2021
52021
Visualizing Cardiolipin In Situ with HKCL-1M, a Highly Selective and Sensitive Fluorescent Probe
W Wang, NK Wong, SL Bok, Y Xu, Y Guo, L Xu, M Zuo, CM St. Croix, ...
Journal of the American Chemical Society 145 (20), 11311-11322, 2023
32023
Structural Achievability of an NH–π Interaction between Gln and Phe in a Crystal Structure of a Collagen-like Peptide
R Zhang, Y Xu, J Lan, S Fan, J Huang, F Xu
Biomolecules 12 (10), 1433, 2022
32022
Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids
YD Hartono, Y Xu, A Karshikoff, L Nilsson, A Villa
Journal of Chemical Information and Modeling 58 (4), 773-783, 2018
32018
An Additive Charmm Force Field for Modified Nucleic Acids
Y Xu, L Nilsson, AD MacKerrel
Biophysical Journal 108 (2), 235a-236a, 2015
12015
Codon recognition on the ribosome-free energy and QM/MM calculations
L Nilsson, A Villa, Y Xu, Y Hartono, M Ito
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46, S206-S206, 2017
2017
Molecular Modeling and Thermodynamics Simulation of Nucleic Acids
Y Xu
PQDT-Global, 2016
2016
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Articles 1–17